Investigations on spreading of PRRSV among swine herds by improved minimum spanning network analysis

Szabó, Péter M.; Szalay, D.; Kecskeméti, Sándor; Molnár, Tamás; Szabó, István; Bálint, Ádám

doi:10.1038/s41598-020-75516-5

Cited by 10 publications

(11 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to understand the origin of the first wave of Hungarian COVID-19 epidemic in 2019 and provide baseline data for the evaluation of future epidemic events we applied a Minimum Spanning Tree-based network analysis on complete genomic sequence data of SARS-CoV-2 available in GISAID database [11] current to April 21. MST analysis is a powerful visualization tool to understand epidemiological patterns during an outbreak situation [8]. The network showed negative exponential degree distribution which is common regarding scale-free networks [21].…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Multiple SARS-CoV-2 Introductions Shaped the Early Outbreak in Central Eastern Europe: Comparing Hungarian Data to a Worldwide Sequence Data-Matrix

Kemenesi

Zeghbib

Somogyi

et al. 2020

Viruses

Self Cite

View full text Add to dashboard Cite

Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019, the situation evolved to pandemic level. Following China, Europe was the second epicenter of the pandemic. To better comprehend the detailed founder mechanisms of the epidemic evolution in Central-Eastern Europe, particularly in Hungary, we determined the full-length SARS-CoV-2 genomes from 32 clinical samples collected from laboratory confirmed COVID-19 patients over the first month of disease in Hungary. We applied a haplotype network analysis on all available complete genomic sequences of SARS-CoV-2 from GISAID database as of 21 April 2020. We performed additional phylogenetic and phylogeographic analyses to achieve the recognition of multiple and parallel introductory events into our region. Here, we present a publicly available network imaging of the worldwide haplotype relations of SARS-CoV-2 sequences and conclude the founder mechanisms of the outbreak in Central-Eastern Europe.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Secondly, the edge weights were transformed (100-weight) in the full network to make high values low and low values high. Next, a minimum spanning tree (MST) was identified as described previously [8]. The path of MST is considered as the most probable chain of infection.…”

Section: Genome Data Analysismentioning

confidence: 99%

Multiple SARS-CoV-2 Introductions Shaped the Early Outbreak in Central Eastern Europe: Comparing Hungarian Data to a Worldwide Sequence Data-Matrix

Kemenesi

Zeghbib

Somogyi

et al. 2020

Viruses

Self Cite

View full text Add to dashboard Cite

show abstract

“…The identification of PRRSV ORF5 and ORF7 sequences provides extremely important information on the spreading of PRRSV, the determination of the possibility of infection and the ways of spreading the epidemic. The visualization of the similarity among the sequences and the visualization of epidemiological relationships significantly enhance the possibility for practitioners to analyse epidemiological processes through virological (molecular biology based) results [ 23 ].…”

Section: Discussionmentioning

confidence: 99%

“…Sequence analysis was performed using the “similarity network” diagram [ 23 ] to identify the closest, most similar sequences to the virus in each vaccine. Subsequently, the percentile similarity of these sequences to ORF5 and ORF7 was evaluated relative to ORF5 and ORF7 of the PRRSV strain of the live virus vaccine tested in GenBank., From 2014 onwards, epidemiological data (veterinary information on the origin of the sample, immunisation etc.)…”

Section: Methodsmentioning

confidence: 99%

Genetic Variability of PRRSV Vaccine Strains Used in the National Eradication Programme, Hungary

et al. 2021

Self Cite

View full text Add to dashboard Cite

Porcine reproductive and respiratory syndrome (PRRS) is a globally spread, highly infectious viral disease. Live, attenuated vaccines against PRRS virus (PRRSV) decrease virus excretion and evoke protective immunity reducing the economic damage caused by the disease. In a longitudinal molecular epidemiological study accompanying ongoing national eradication programme we evaluated the suitability of PRRSV ORF5 and ORF7 sequences to identify possible field strains of vaccine-origin. In total, 2342 ORF5 sequences and 478 ORF7 sequences were analysed. Vaccine strains were identified by sequence identity values and phylogenetic network analysis. Strains that shared greater than 98% nucleotide identity within ORF5 and/or ORF7 were considered to have originated from vaccine. A total of 882 (37.6%) ORF5 and 88 (18.4%) ORF7 sequences met these criteria. In detail, 618, 179 and 35 ORF5 and 51, 29 and 8 ORF7 sequences were related to Porcilis PRRS vaccine, Unistrain PRRS vaccine, and ReproCyc PRRS EU vaccine, respectively. Data showed that the Porcilis vaccine was genetically more stable. Whereas, the variability of the Unistrain and the ReproCyc strains was significantly higher. Given that ORF7 shares, in some instances, complete identity between a particular vaccine strain and some historic variants of field PRRSV strains, care must be taken when evaluating vaccine relatedness of a field isolate based on the ORF7. On the contrary, ORF5 sequences were more suitable to predict the vaccine origin making a distinction more robustly between field and vaccine strains. We conclude that ORF5 based molecular epidemiological studies support more efficiently the ongoing PRRS eradication programmes. The conclusions presented in this large-scale PRRS molecular epidemiological study provides a framework for future eradication programmes planned in other countries.

show abstract

“…Chromatograms were analysed and edited manually using the BioEdit software version 7.2, available at http://www.mbio.ncsu.edu/BioEdit/bioedit.html [22]. Based on the sequence data, the 'similarity network' image was performed [23] and the sequences were classi ed as described by Shi et al [24] and Balka et al [25]. For the similarity network analysis, a total of 2,966 PRRSV ORF5 sequences were identi ed in Hungary from 2003 onwards.…”

Section: Methodsmentioning

confidence: 99%

Eradication of PRRS from Hungarian pig herds 2014–2022

Szabó¹,

Nemes²,

Bognár

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Porcine reproductive and respiratory syndrome (PRRS) is an infectious disease with widespread distribution and is currently a major cause of economic loss in pig production. In Hungary, a National PRRS Eradication Program was introduced in order to reach a more efficient, economic and competitive international market position. The EU also approved the program, but the resultant legal obligations placed a burden on Hungarian producers in order to comply with EU competition rules. The veterinary authorities carried out the implementation of the program with the consent, continuous support and monitoring by the organizations of the pig industry as well as a scientific committee. The PRRS eradication program in Hungary was based on a regional territorial principle and was obligatory for every swine farm within those regions. In Hungary large fattening farms operate as all-in/all-out or continuous flow system. The large-scale breeding herds are predominantly farrow-to-finish types. Although its significance has decreased in recent decades, 20% of the Hungarian pig population is still kept in small-scale (backyard) farms (< 100 animals). Each PRRS-infected large-scale farm had to develop a unit-adapted eradication plan, including external and internal biosecurity measures, vaccinations, etc. It was crucial to render each fattening unit free of the disease since fattening units play a significant role in spreading the virus across the country. Eradication efforts mainly implemented depopulation-repopulation methods, with some farms using the test and removal method instead. Results: As the eradication progressed over the years, the introduction of infected fattening pigs was restricted. Because of these measures, by the end of 2018, Hungarian large-scale fattening farms became free of PRRS. The PRRS-free status of the small-scale herds was achieved by the end of 2015, and this status was maintained from 2016–2021. By the 31st of December in 2021, all breeding pigs at large scale-farms in Hungary had become free of wild type PRRS virus. By the 31st of March in 2022, the total pig population of the country, including all backyard farms and fattening units, had achieved PRRS-free status. Conclusions: The future goal is to secure and maintain the PRRS free status of Hungary by strict import regulations of live animals combined with continuous and thorough screening of incoming and resident herds for the presence of the virus.

show abstract

Investigations on spreading of PRRSV among swine herds by improved minimum spanning network analysis

Cited by 10 publications

References 28 publications

Multiple SARS-CoV-2 Introductions Shaped the Early Outbreak in Central Eastern Europe: Comparing Hungarian Data to a Worldwide Sequence Data-Matrix

Multiple SARS-CoV-2 Introductions Shaped the Early Outbreak in Central Eastern Europe: Comparing Hungarian Data to a Worldwide Sequence Data-Matrix

Genetic Variability of PRRSV Vaccine Strains Used in the National Eradication Programme, Hungary

Eradication of PRRS from Hungarian pig herds 2014–2022

Contact Info

Product

Resources

About